Hi,
I'm trying to do the simple volume rendering from the cookbook. The data is
FLASH HDF5 data, and I'm using version 3.0.2 of yt. The script I'm running
is here:
http://paste.yt-project.org/show/5183/
However, I'm getting the following error:
http://paste.yt-project.org/show/5184/
I guess it has something to do with the AMR tree, but unfortunately I don't
know a lot about the specifics of that.
Could anyone offer any insight into this problem?
Thanks,
Daniel

Dear all,
I am trying to make a phase plot using YT 2.6, with the following line.
*plot = PhasePlot(my_sphere, "Density**", "**Temperature*
*","CellMassMsun",weight_field=None,x_log=1,y_log=1).save()*
but it is giving me the following error.
*plot = PhasePlot(my_sphere, "MachNumber",
"CRFractionPreCR","CellMassMsun",weight_field=None,x_log=1,y_log=1).save()*
*TypeError: __init__() got an unexpected keyword argument 'x_log'*
I also tried with x_log=True.Still the same error. What could be the
problem? How to make both x and y in log scale?
And also I would like to know is it possible to fix x and y range in phase
plot?
Thank you.
--
Reju Sam John

Hi all,
Is there a way to specify the log/non-log scaling of a y-axis variable in create_profile or ProfilePlot.from_profiles? I have some profiles that start flat at an initial time and so the velocity_magnitude is everywhere 0. create_profile succeeds, but ProfilePlot.from_profiles generates a Matplotlib error before I have the ability to specify a scaling:
sph = ds.sphere(ds.domain_center, ds.domain_width[0]/2)
profile = yt.create_profile(sph, "radius",
["density", "temperature", "velocity_magnitude", "dx"],
extrema={'radius':(ds.domain_width[0]/ds.num_grid,ds.domain_width[0]/2.)},
n_bins=int(ds.domain_width[0]*2.**(ds.max_level-1)),
logs={'radius':False},
units={'radius':'pc'})
plot = yt.ProfilePlot.from_profiles(profile)
Relevant part of the dump:
/software/python-2.7-2014q3-el6-x86_64/lib/python2.7/site-packages/matplotlib-1.4.0-py2.7-linux-x86_64.egg/matplotlib/ticker.pyc in view_limits(self, vmin, vmax)
1523 if minpos <= 0 or not np.isfinite(minpos):
1524 raise ValueError(
-> 1525 "Data has no positive values, and therefore can not be "
1526 "log-scaled.")
1527
Douglas Rudd
Scientific Computing Consultant
Research Computing Center
drudd(a)uchicago.edu

Hi,
I am using the code yt.lagrangian_volume to trace the box that contains the
dark matter particles at an early stage(higher redshift). But I was quite
confused about the output. I am attaching the output file below.
(1) I don't know what the values for the box in the new frame mean, i.e.
what is the unit of these values? It seems to be the normalized scale
because the values are about 1. But it does not seem to be normalized too
because there are some values that are larger than 1. Is that due to the
periodicity of the box?
(2) The bounding box and box in the new frame seems to have the same size.
The difference between the two box is just translation. But I was expecting
that the box should be expanding/collapsing.
(3) The COM (center of mass) in the output is within neither of the box.
Does anyone know how to explain the box values in the output file?
Thanks,
Jingjing
--
Jingjing Chen [ chenjj235(a)gmail.com ]
Department of Astronomy
Columbia University
550 West 120th Street
New York, New York 10027
Cell Phone: +1(347)5746709

Hi,
I am using the code yt.lagrangian_volume to trace the box that contains the
dark matter particles at an early stage(higher redshift). But I was quite
confused about the output. I am attaching the output file below.
(1) I don't know what the values for the box in the new frame mean, i.e.
what is the unit of these values? It seems to be the normalized scale
because the values are about 1. But it does not seem to be normalized too
because there are some values that are larger than 1. Is that due to the
periodicity of the box?
(2) The bounding box and box in the new frame seems to have the same size.
The difference between the two box is just translation. But I was expecting
that the box should be expanding/collapsing.
(3) The COM (center of mass) in the output is within neither of the box.
Does anyone know how to explain the box values in the output file?
Thanks,
Jingjing
--
Jingjing Chen [ chenjj235(a)gmail.com ]
Department of Astronomy
Columbia University
550 West 120th Street
New York, New York 10027
Cell Phone: +1(347)5746709

Dear all,
This might be a stupid question but I’m trying for a few hours to add lines to a PhasePlot I have created.
Everything I tried so far failed and I was only able to find some instructions using PlotCollection which is outdated.
Is there an easy solution?
Thanks and kind regards,
Stefanie

This might be of interest here.
---------- Forwarded message ----------
From: *Robert Thompson* <rthompsonj(a)gmail.com>
Date: Sunday, October 26, 2014
Subject: [gadget-list] universal reader for python
To: gadget-list(a)mpa-garching.mpg.de
Gadget community,
I wanted to share a tool that I’ve been developing for the past several
years called pyGadgetReader. It is a universal gadget snapshot reader for
python that supports type-1, type-2, HDF5, and TIPSY binary outputs (also
supports binaries from FoF, P-StarGroupFinder, Rockstar, &
Rockstar-Galaxies). I finally got around to polishing up the documentation
and now believe it to be ready for public consumption. Happy simulating!
https://bitbucket.org/rthompson/pygadgetreader
-Robert Thompson

Hi all,
I have some outputs from an unknown (private) branch of Enzo (possibly as
early as version 1.5). I believe there was no big change on the output
structure vs actual Enzo 1.5. When loaded it with yt (3.0.2), I got an
empty field list. Can someone point me to where I can look at? Thanks a lot!
Best,
Kit
--
Wing Kit Lee
Postdoc Fellow
Academia Sinica, Institute of Astronomy and Astrophysics